Nucleoid, bacterial

Bacterial cells share certain common structural features, but also show group-specific specializations (Fig. 1-6). E. coli is a usually harmless inhabitant of the human intestinal tract. The E. coli cell is about 2 prri long and a little less than 1 prri in diameter. It has a protective outer membrane and an inner plasma membrane that encloses the cytoplasm and the nucleoid. Between the inner and outer membranes is a thin but strong layer of polymers called peptidoglycans, which gives the cell its shape and rigidity. The plasma membrane and the... 

Bacterial cells contain cytosol, a nucleoid, and plasmids. Eukaryotic cells have a nucleus and are multicompartmented, segregating certain processes in specific organelles, which can be separated and studied in isolation. 

As in the case of protein structure (Chapter 4), it is sometimes useful to describe nucleic acid structure in terms of hierarchical levels of complexity (primary, secondary, tertiary). The primary structure of a nucleic acid is its covalent structure and nucleotide sequence. Any regular, stable structure taken up by some or all of the nucleotides in a nucleic acid can be referred to as secondary structure. All structures considered in the remainder of this chapter fall under the heading of secondary structure. The complex folding of large chromosomes within eukaryotic chromatin and bacterial nucleoids is generally considered tertiary structure this is discussed in Chapter 24. 

We now turn briefly to the structure of bacterial chromosomes. Bacterial DNA is compacted in a structure called the nucleoid, which can occupy a significant... 

Bacterial chromosomes are also extensively compacted into the nucleoid, but the chromosome appears to be much more dynamic and irregular in structure than eukaryotic chromatin, reflecting the shorter cell cycle and very active metabolism of a bacterial cell. 

If bacterial cells are lysed under certain conditions, e.g., in 1 M NaCl or in the presence of a "physiological" 5 mM spermidine, the entire bacterial chromosome can be isolated.10 The DNA in these isolated chromosomes retains some torsional tension that, however, can be relaxed by nicking with nucleases or by y-irradiation. However, a single nick relaxes the DNA very little. The explanation appears to be that the DNA is held by proteins of the nucleoid matrix in a series of loops (Fig. 27-2). A single nick relaxes just... 

The DNA of a bacterial cell, such as Escherichia coli, is a circular double-stranded molecule often referred to as the bacterial chromosome. In E. coli this DNA molecule contains 4.6 million base pairs. The circular DNA is packaged into a region of the cell called the nucleoid (see Topic Al) where it is organized into 50 or so loops or domains that are bound to a central protein scaffold, attached to the cell membrane. Fig. la illustrates this organization, although only six loops are shown for clarity. Within this structure, the DNA is actually not a circular double-stranded DNA molecule such as that shown in Fig. lb but is negatively supercoiled, that is, it is twisted upon itself (Fig. lc) and is also complexed with several DNA-binding proteins, the most common of which are proteins HU, HLP-1 and H-NS. These are histone-like proteins (see below for a description of histones). 

A highly compact structure can be isolated that contains a single, supercoiled DNA molecule and protein. This is the bacterial chromosome or nucleoid. Because removal of protein decreases the compactness of this structure, it is concluded that the protein acts as a scaffold to keep the nucleoid in a compact state by binding to specific regions of the DNA molecule. The nucleoid DNA is also attached to the cytoplasmic membrane. 

In eukaryotes, DNA does not exist free. It is complexed with an approximately equal mass of basic proteins called histones. For a long time it was thought that bacterial DNA did not form such complexes. While histones are absent from bacteria, there is increasing evidence for the presence of histonelike proteins in them that enable condensation of their DNA into its compact nucleoid form. 

In bacterial cells, there is no membrane surrounding the DNA nucleoid, and both DNA transcription and RNA translation proceed within the single cell compartment. In eukaryotes, the nucleus is bounded by a membrane (Chap. 1). Transcription occurs within the nucleus, and the mRNA must pass into the cytoplasm, where it is translated. Frequently, the immediate polypeptide product of translation is subsequently modified, sometimes in a process that enables it to be transported out of the cell in which it is made. 

Isolated Bacterial Nucleoids, Characterization, Assay, and Use of (Hirschbein... 

Cytoplasm - The cytoplasm, or protoplasm, of bacterial cells is where the functions for cell growth, metabolism, and replication are carried out. It is a gellike matrix composed of water, enzymes, nutrients, wastes, and gases and contains cell structures such as ribosomes, a chromosome, and plasmids. The cell envelope encases the cytoplasm and all its components. Unlike the eukaryotic (true) cells, bacteria do not have a membrane enclosed nucleus. The chromosome, a single, continuous strand of DNA, is localized, but not contained, in a region of the cell called the nucleoid. All the other cellular components are scattered throughout the cytoplasm. 

A FIGURE 1-2 Prokaryotic cells have a simpler internal organization than eukaryotic cells, (a) Electron micrograph of a thin section of Escherichia coii, a common intestinal bacterium. The nucleoid, consisting of the bacterial DNA, is not enclosed within a membrane. E. coii and some other bacteria are surrounded by two membranes separated by the periplasmic space. The thin cell wall is adjacent to the inner membrane. 

Isolated Bacterial Nucleoids Hjerten, S., see Porath, J. Hjerten, Slellan, Free Zone Electrophoresis. Theory, Equipment 28 297... 

Prokaryotes - Prokaryotic mRNAs are synthesized on the bacterial nucleoid in direct contact with the cytosol and are immediately available for translation. The Shine-Dalgamo sequence (see here) near the 5 end of the mRNA binds to a site on the prokaryotic ribosomal RNA (rRNA), allowing attachment of the ribosome and initiation of translation, often even before transcription is completed. 

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